Arrayed Primer Extension Resequencing of Mutations in the TP53 Tumor Suppressor Gene: Comparison with Denaturing HPLC and Direct Sequencing

Mutations of TP53 (17p13.1; OMIM 191170; PubMed accession number X54156) are common in cancers and are typically missense within exons 4–9, impairing the capacity of p53 to transactivate genes involved in cell cycle arrest, apoptosis, and DNA repair (1). Functionally, mutations may differ according to their nature and position, as well as to the presence of a common polymorphism at codon 72 (arginine or a proline) in the mutant allele (2). Knowing TP53 mutation status has potential applications for cancer prognosis (3)(4) and early diagnosis (5), identification of mutagen “fingerprints” (1)(6), and prediction of therapeutic outcomes (7)(8). To achieve this purpose, sensitive, fast, and cost-effective methods are needed to assess the whole coding sequence plus exon/intron boundaries. Current approaches are based on mutation prescreening with single strand conformational polymorphism analysis, temporal temperature gradient electrophoresis, or denaturing HPLC (DHPLC) combined with direct sequencing of relevant PCR fragments [reviewed in Ref. (9)]. These methods are labor-intensive, difficult to standardize, and in some cases, of limited sensitivity. In recent years, 2 microarray methods for resequencing TP53 have been described: the Affymetrix p53 GeneChip array, described elsewhere (10)(11), and the Arrayed Primer Extension (APEX), based on incorporation of 4 dye terminators into oligonucleotide primers that each identify a base in the target sequence (12). In 2002, we described an APEX array for resequencing TP53 exons 2–9, which contain 95% of known mutations in TP53 (13). Here we compare the sensitivity and detection limits of APEX with a standard method, DHPLC/direct sequencing, and discuss the potential of APEX for application to cancer diagnostic or prognostic purposes.Specimens in the comparison set included 6 cell lines with mutations in different TP53 exons (see Table 1 of the Data Supplement that accompanies the online version of this Technical …